Buggy code:
public class CommandLine { protected static String _versinon = "4.5.1" ; private static void exitWithErr ( String extraMessage , SimpleJSAP jsap ) { } private static SimpleJSAP getJSAP ( ) throws JSAPException { <START_BUG> return new SimpleJSAP ( ( ( "ASTRAL<seq2seq4repair_space>(version" + ( CommandLine . _versinon ) ) + ")" ) , ( "species<seq2seq4repair_space>tree<seq2seq4repair_space>inference<seq2seq4repair_space>from<seq2seq4repair_space>unrooted<seq2seq4repair_space>gene<seq2seq4repair_space>trees.<seq2seq4repair_space>" + ( ( ( "The<seq2seq4repair_space>ASTRAL<seq2seq4repair_space>algorithm<seq2seq4repair_space>maximizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>shared<seq2seq4repair_space>quartet<seq2seq4repair_space>trees<seq2seq4repair_space>with" + "<seq2seq4repair_space>the<seq2seq4repair_space>collection<seq2seq4repair_space>of<seq2seq4repair_space>all<seq2seq4repair_space>gene<seq2seq4repair_space>trees.<seq2seq4repair_space>The<seq2seq4repair_space>result<seq2seq4repair_space>of<seq2seq4repair_space>this<seq2seq4repair_space>optimization<seq2seq4repair_space>problem" ) + "<seq2seq4repair_space>is<seq2seq4repair_space>statistically<seq2seq4repair_space>consistent<seq2seq4repair_space>under<seq2seq4repair_space>the<seq2seq4repair_space>multi-species<seq2seq4repair_space>coalesent<seq2seq4repair_space>model." ) + "<seq2seq4repair_space>This<seq2seq4repair_space>software<seq2seq4repair_space>can<seq2seq4repair_space>also<seq2seq4repair_space>solve<seq2seq4repair_space>MGD<seq2seq4repair_space>and<seq2seq4repair_space>MGDL<seq2seq4repair_space>problems<seq2seq4repair_space>(see<seq2seq4repair_space>options)<seq2seq4repair_space>instead<seq2seq4repair_space>of<seq2seq4repair_space>ASTRAL." ) ) , new Parameter [ ] { new FlaggedOption ( "input<seq2seq4repair_space>file" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . REQUIRED , 'i' , "input" , "a<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>input<seq2seq4repair_space>gene<seq2seq4repair_space>trees<seq2seq4repair_space>in<seq2seq4repair_space>newick<seq2seq4repair_space>format.<seq2seq4repair_space>(required)" ) , new FlaggedOption ( "output<seq2seq4repair_space>file" , FileStringParser . getParser ( ) , null , JSAP . NOT_REQUIRED , 'o' , "output" , "a<seq2seq4repair_space>filename<seq2seq4repair_space>for<seq2seq4repair_space>storing<seq2seq4repair_space>the<seq2seq4repair_space>output<seq2seq4repair_space>species<seq2seq4repair_space>tree.<seq2seq4repair_space>Defaults<seq2seq4repair_space>to<seq2seq4repair_space>outputting<seq2seq4repair_space>to<seq2seq4repair_space>stdout." ) , new Switch ( "exact" , 'x' , "exact" , "find<seq2seq4repair_space>the<seq2seq4repair_space>exact<seq2seq4repair_space>solution<seq2seq4repair_space>by<seq2seq4repair_space>looking<seq2seq4repair_space>at<seq2seq4repair_space>all<seq2seq4repair_space>clusters<seq2seq4repair_space>-<seq2seq4repair_space>recommended<seq2seq4repair_space>only<seq2seq4repair_space>for<seq2seq4repair_space>small<seq2seq4repair_space>(<18)<seq2seq4repair_space>numer<seq2seq4repair_space>of<seq2seq4repair_space>taxa." ) , new FlaggedOption ( "extra<seq2seq4repair_space>trees" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'e' , "extra" , "provide<seq2seq4repair_space>extra<seq2seq4repair_space>trees<seq2seq4repair_space>(with<seq2seq4repair_space>gene<seq2seq4repair_space>labels)<seq2seq4repair_space>used<seq2seq4repair_space>to<seq2seq4repair_space>enrich<seq2seq4repair_space>the<seq2seq4repair_space>set<seq2seq4repair_space>of<seq2seq4repair_space>clusters<seq2seq4repair_space>searched" ) , new FlaggedOption ( "extra<seq2seq4repair_space>species<seq2seq4repair_space>trees" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'f' , "extra-species" , "provide<seq2seq4repair_space>extra<seq2seq4repair_space>trees<seq2seq4repair_space>(with<seq2seq4repair_space>species<seq2seq4repair_space>lables)<seq2seq4repair_space>used<seq2seq4repair_space>to<seq2seq4repair_space>enrich<seq2seq4repair_space>the<seq2seq4repair_space>set<seq2seq4repair_space>of<seq2seq4repair_space>clusters<seq2seq4repair_space>searched" ) , new FlaggedOption ( "bootstraps" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'b' , "bootstraps" , ( "perform<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping<seq2seq4repair_space>using<seq2seq4repair_space>input<seq2seq4repair_space>bootstrap<seq2seq4repair_space>replicate<seq2seq4repair_space>files<seq2seq4repair_space>(use<seq2seq4repair_space>--rep<seq2seq4repair_space>to<seq2seq4repair_space>change<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>replications).<seq2seq4repair_space>" + ( "The<seq2seq4repair_space>file<seq2seq4repair_space>given<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option<seq2seq4repair_space>should<seq2seq4repair_space>have<seq2seq4repair_space>a<seq2seq4repair_space>list<seq2seq4repair_space>of<seq2seq4repair_space>the<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>bootstrap<seq2seq4repair_space>files,<seq2seq4repair_space>one<seq2seq4repair_space>per<seq2seq4repair_space>line,<seq2seq4repair_space>and<seq2seq4repair_space>each<seq2seq4repair_space>line<seq2seq4repair_space>corresponding<seq2seq4repair_space>to<seq2seq4repair_space>one<seq2seq4repair_space>gene.<seq2seq4repair_space>" + "By<seq2seq4repair_space>default<seq2seq4repair_space>performs<seq2seq4repair_space>site-only<seq2seq4repair_space>resampling,<seq2seq4repair_space>but<seq2seq4repair_space>gene<seq2seq4repair_space>only<seq2seq4repair_space>resampling<seq2seq4repair_space>can<seq2seq4repair_space>also<seq2seq4repair_space>be<seq2seq4repair_space>used.<seq2seq4repair_space>" ) ) ) , new FlaggedOption ( "replicates" , JSAP . INTEGER_PARSER , "100" , JSAP . NOT_REQUIRED , 'r' , "reps" , "Set<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>bootstrap<seq2seq4repair_space>replicates<seq2seq4repair_space>done<seq2seq4repair_space>in<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping.<seq2seq4repair_space>" ) , new FlaggedOption ( "seed" , JSAP . LONG_PARSER , "692" , JSAP . NOT_REQUIRED , 's' , "seed" , "Set<seq2seq4repair_space>the<seq2seq4repair_space>seed<seq2seq4repair_space>number<seq2seq4repair_space>used<seq2seq4repair_space>in<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping.<seq2seq4repair_space>" ) , new Switch ( "gene-sampling" , 'g' , "gene-resampling" , "perform<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>resampling<seq2seq4repair_space>in<seq2seq4repair_space>addition<seq2seq4repair_space>to<seq2seq4repair_space>site<seq2seq4repair_space>resampling.<seq2seq4repair_space>Useful<seq2seq4repair_space>only<seq2seq4repair_space>with<seq2seq4repair_space>the<seq2seq4repair_space>-b<seq2seq4repair_space>option." ) , new FlaggedOption ( "mapping<seq2seq4repair_space>file" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'a' , "namemapfile" , ( "a<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>the<seq2seq4repair_space>mapping<seq2seq4repair_space>between<seq2seq4repair_space>names<seq2seq4repair_space>in<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>and<seq2seq4repair_space>names<seq2seq4repair_space>in<seq2seq4repair_space>the<seq2seq4repair_space>species<seq2seq4repair_space>tree.<seq2seq4repair_space>" + ( ( "The<seq2seq4repair_space>mapping<seq2seq4repair_space>file<seq2seq4repair_space>has<seq2seq4repair_space>one<seq2seq4repair_space>line<seq2seq4repair_space>per<seq2seq4repair_space>species,<seq2seq4repair_space>with<seq2seq4repair_space>one<seq2seq4repair_space>of<seq2seq4repair_space>two<seq2seq4repair_space>formats:\n" + "<seq2seq4repair_space>species:<seq2seq4repair_space>gene1,gene2,gene3,gene4\n" ) + "<seq2seq4repair_space>species<seq2seq4repair_space>4<seq2seq4repair_space>gene1<seq2seq4repair_space>gene2<seq2seq4repair_space>gene3<seq2seq4repair_space>gene4\n" ) ) ) , new Switch ( "duplication" , 'd' , "dup" , ( "Solves<seq2seq4repair_space>MGD<seq2seq4repair_space>problem.<seq2seq4repair_space>Minimizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>duplications<seq2seq4repair_space>required<seq2seq4repair_space>to<seq2seq4repair_space>explain<seq2seq4repair_space>" + ( "gene<seq2seq4repair_space>trees<seq2seq4repair_space>using<seq2seq4repair_space>DynaDup<seq2seq4repair_space>algorithm<seq2seq4repair_space>(Bayzid,<seq2seq4repair_space>2011).<seq2seq4repair_space>Note<seq2seq4repair_space>that<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option,<seq2seq4repair_space>" + "DynaDyp<seq2seq4repair_space>would<seq2seq4repair_space>be<seq2seq4repair_space>used<seq2seq4repair_space>*instead<seq2seq4repair_space>of*<seq2seq4repair_space>ASTRAL." ) ) ) , new FlaggedOption ( "duploss<seq2seq4repair_space>weight" , JSAP . STRING_PARSER , null , JSAP . NOT_REQUIRED , 'l' , "duploss" , ( "Solves<seq2seq4repair_space>MGDL<seq2seq4repair_space>problem.<seq2seq4repair_space>Minimizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>duplication<seq2seq4repair_space>and<seq2seq4repair_space>losses<seq2seq4repair_space>required" + ( ( ( ( "<seq2seq4repair_space>to<seq2seq4repair_space>explain<seq2seq4repair_space>gene<seq2seq4repair_space>trees<seq2seq4repair_space>using<seq2seq4repair_space>DynaDup<seq2seq4repair_space>algorithm.<seq2seq4repair_space>Note<seq2seq4repair_space>that<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option,<seq2seq4repair_space>" + "DynaDyp<seq2seq4repair_space>would<seq2seq4repair_space>be<seq2seq4repair_space>used<seq2seq4repair_space>*instead<seq2seq4repair_space>of*<seq2seq4repair_space>ASTRAL.<seq2seq4repair_space>" ) + "Use<seq2seq4repair_space>-l<seq2seq4repair_space>0<seq2seq4repair_space>for<seq2seq4repair_space>standard<seq2seq4repair_space>(homomorphic)<seq2seq4repair_space>definition,<seq2seq4repair_space>and<seq2seq4repair_space>-l<seq2seq4repair_space>1<seq2seq4repair_space>for<seq2seq4repair_space>our<seq2seq4repair_space>new<seq2seq4repair_space>bd<seq2seq4repair_space>definition.<seq2seq4repair_space>" ) + "Any<seq2seq4repair_space>value<seq2seq4repair_space>in<seq2seq4repair_space>between<seq2seq4repair_space>weights<seq2seq4repair_space>the<seq2seq4repair_space>impact<seq2seq4repair_space>of<seq2seq4repair_space>missing<seq2seq4repair_space>taxa<seq2seq4repair_space>somewhere<seq2seq4repair_space>between<seq2seq4repair_space>these<seq2seq4repair_space>two<seq2seq4repair_space>extremes.<seq2seq4repair_space>" ) + "-l<seq2seq4repair_space>auto<seq2seq4repair_space>will<seq2seq4repair_space>automaticaly<seq2seq4repair_space>pick<seq2seq4repair_space>this<seq2seq4repair_space>weight.<seq2seq4repair_space>" ) ) ) } ) ; <END_BUG> } public static void main ( String [ ] args ) throws Exception { } private static Tree runOnOneInput ( int criterion , boolean rooted , boolean extrarooted , List < Tree > extraTrees , double cs , double cd , double wh , boolean exact , BufferedWriter outbuffer , List < Tree > input , Iterable < Tree > bootstraps , String outgroup ) { } private static Inference initializeInference ( int criterion , boolean rooted , boolean extrarooted , List < Tree > trees , List < Tree > extraTrees , double cs , double cd , double wh , boolean exact ) { } private static void readInputTrees ( BufferedReader treeBufferReader , boolean rooted , List < Tree > trees , boolean checkCompleteness , boolean stLablel ) throws FileNotFoundException , IOException { } private static void writeSolutionToFile ( BufferedWriter outbuffer , List < Solution > solutions , String outgroup ) { } }

Fix:
return new SimpleJSAP ( ( ( "ASTRAL<seq2seq4repair_space>(version" + ( CommandLine . _versinon ) ) + ")" ) , ( "species<seq2seq4repair_space>tree<seq2seq4repair_space>inference<seq2seq4repair_space>from<seq2seq4repair_space>unrooted<seq2seq4repair_space>gene<seq2seq4repair_space>trees.<seq2seq4repair_space>" + ( ( ( "The<seq2seq4repair_space>ASTRAL<seq2seq4repair_space>algorithm<seq2seq4repair_space>maximizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>shared<seq2seq4repair_space>quartet<seq2seq4repair_space>trees<seq2seq4repair_space>with" + "<seq2seq4repair_space>the<seq2seq4repair_space>collection<seq2seq4repair_space>of<seq2seq4repair_space>all<seq2seq4repair_space>gene<seq2seq4repair_space>trees.<seq2seq4repair_space>The<seq2seq4repair_space>result<seq2seq4repair_space>of<seq2seq4repair_space>this<seq2seq4repair_space>optimization<seq2seq4repair_space>problem" ) + "<seq2seq4repair_space>is<seq2seq4repair_space>statistically<seq2seq4repair_space>consistent<seq2seq4repair_space>under<seq2seq4repair_space>the<seq2seq4repair_space>multi-species<seq2seq4repair_space>coalesent<seq2seq4repair_space>model." ) + "<seq2seq4repair_space>This<seq2seq4repair_space>software<seq2seq4repair_space>can<seq2seq4repair_space>also<seq2seq4repair_space>solve<seq2seq4repair_space>MGD<seq2seq4repair_space>and<seq2seq4repair_space>MGDL<seq2seq4repair_space>problems<seq2seq4repair_space>(see<seq2seq4repair_space>options)<seq2seq4repair_space>instead<seq2seq4repair_space>of<seq2seq4repair_space>ASTRAL." ) ) , new Parameter [ ] { new FlaggedOption ( "input<seq2seq4repair_space>file" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . REQUIRED , 'i' , "input" , "a<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>input<seq2seq4repair_space>gene<seq2seq4repair_space>trees<seq2seq4repair_space>in<seq2seq4repair_space>newick<seq2seq4repair_space>format.<seq2seq4repair_space>(required)" ) , new FlaggedOption ( "output<seq2seq4repair_space>file" , FileStringParser . getParser ( ) , null , JSAP . NOT_REQUIRED , 'o' , "output" , "a<seq2seq4repair_space>filename<seq2seq4repair_space>for<seq2seq4repair_space>storing<seq2seq4repair_space>the<seq2seq4repair_space>output<seq2seq4repair_space>species<seq2seq4repair_space>tree.<seq2seq4repair_space>Defaults<seq2seq4repair_space>to<seq2seq4repair_space>outputting<seq2seq4repair_space>to<seq2seq4repair_space>stdout." ) , new Switch ( "exact" , 'x' , "exact" , "find<seq2seq4repair_space>the<seq2seq4repair_space>exact<seq2seq4repair_space>solution<seq2seq4repair_space>by<seq2seq4repair_space>looking<seq2seq4repair_space>at<seq2seq4repair_space>all<seq2seq4repair_space>clusters<seq2seq4repair_space>-<seq2seq4repair_space>recommended<seq2seq4repair_space>only<seq2seq4repair_space>for<seq2seq4repair_space>small<seq2seq4repair_space>(<18)<seq2seq4repair_space>numer<seq2seq4repair_space>of<seq2seq4repair_space>taxa." ) , new FlaggedOption ( "extra<seq2seq4repair_space>trees" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'e' , "extra" , "provide<seq2seq4repair_space>extra<seq2seq4repair_space>trees<seq2seq4repair_space>(with<seq2seq4repair_space>gene<seq2seq4repair_space>labels)<seq2seq4repair_space>used<seq2seq4repair_space>to<seq2seq4repair_space>enrich<seq2seq4repair_space>the<seq2seq4repair_space>set<seq2seq4repair_space>of<seq2seq4repair_space>clusters<seq2seq4repair_space>searched" ) , new FlaggedOption ( "extra<seq2seq4repair_space>species<seq2seq4repair_space>trees" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'f' , "extra-species" , "provide<seq2seq4repair_space>extra<seq2seq4repair_space>trees<seq2seq4repair_space>(with<seq2seq4repair_space>species<seq2seq4repair_space>lables)<seq2seq4repair_space>used<seq2seq4repair_space>to<seq2seq4repair_space>enrich<seq2seq4repair_space>the<seq2seq4repair_space>set<seq2seq4repair_space>of<seq2seq4repair_space>clusters<seq2seq4repair_space>searched" ) , new FlaggedOption ( "bootstraps" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'b' , "bootstraps" , ( "perform<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping<seq2seq4repair_space>using<seq2seq4repair_space>input<seq2seq4repair_space>bootstrap<seq2seq4repair_space>replicate<seq2seq4repair_space>files<seq2seq4repair_space>(use<seq2seq4repair_space>--rep<seq2seq4repair_space>to<seq2seq4repair_space>change<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>replications).<seq2seq4repair_space>" + ( "The<seq2seq4repair_space>file<seq2seq4repair_space>given<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option<seq2seq4repair_space>should<seq2seq4repair_space>have<seq2seq4repair_space>a<seq2seq4repair_space>list<seq2seq4repair_space>of<seq2seq4repair_space>the<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>bootstrap<seq2seq4repair_space>files,<seq2seq4repair_space>one<seq2seq4repair_space>per<seq2seq4repair_space>line,<seq2seq4repair_space>and<seq2seq4repair_space>each<seq2seq4repair_space>line<seq2seq4repair_space>corresponding<seq2seq4repair_space>to<seq2seq4repair_space>one<seq2seq4repair_space>gene.<seq2seq4repair_space>" + "By<seq2seq4repair_space>default<seq2seq4repair_space>performs<seq2seq4repair_space>site-only<seq2seq4repair_space>resampling,<seq2seq4repair_space>but<seq2seq4repair_space>gene//site<seq2seq4repair_space>resampling<seq2seq4repair_space>can<seq2seq4repair_space>also<seq2seq4repair_space>be<seq2seq4repair_space>used.<seq2seq4repair_space>" ) ) ) , new FlaggedOption ( "replicates" , JSAP . INTEGER_PARSER , "100" , JSAP . NOT_REQUIRED , 'r' , "reps" , "Set<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>of<seq2seq4repair_space>bootstrap<seq2seq4repair_space>replicates<seq2seq4repair_space>done<seq2seq4repair_space>in<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping.<seq2seq4repair_space>" ) , new FlaggedOption ( "seed" , JSAP . LONG_PARSER , "692" , JSAP . NOT_REQUIRED , 's' , "seed" , "Set<seq2seq4repair_space>the<seq2seq4repair_space>seed<seq2seq4repair_space>number<seq2seq4repair_space>used<seq2seq4repair_space>in<seq2seq4repair_space>multi-locus<seq2seq4repair_space>bootstrapping.<seq2seq4repair_space>" ) , new Switch ( "gene-sampling" , 'g' , "gene-resampling" , "perform<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>resampling<seq2seq4repair_space>in<seq2seq4repair_space>addition<seq2seq4repair_space>to<seq2seq4repair_space>site<seq2seq4repair_space>resampling.<seq2seq4repair_space>Useful<seq2seq4repair_space>only<seq2seq4repair_space>with<seq2seq4repair_space>the<seq2seq4repair_space>-b<seq2seq4repair_space>option." ) , new FlaggedOption ( "mapping<seq2seq4repair_space>file" , FileStringParser . getParser ( ) . setMustExist ( true ) , null , JSAP . NOT_REQUIRED , 'a' , "namemapfile" , ( "a<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>the<seq2seq4repair_space>mapping<seq2seq4repair_space>between<seq2seq4repair_space>names<seq2seq4repair_space>in<seq2seq4repair_space>gene<seq2seq4repair_space>tree<seq2seq4repair_space>and<seq2seq4repair_space>names<seq2seq4repair_space>in<seq2seq4repair_space>the<seq2seq4repair_space>species<seq2seq4repair_space>tree.<seq2seq4repair_space>" + ( ( "The<seq2seq4repair_space>mapping<seq2seq4repair_space>file<seq2seq4repair_space>has<seq2seq4repair_space>one<seq2seq4repair_space>line<seq2seq4repair_space>per<seq2seq4repair_space>species,<seq2seq4repair_space>with<seq2seq4repair_space>one<seq2seq4repair_space>of<seq2seq4repair_space>two<seq2seq4repair_space>formats:\n" + "<seq2seq4repair_space>species:<seq2seq4repair_space>gene1,gene2,gene3,gene4\n" ) + "<seq2seq4repair_space>species<seq2seq4repair_space>4<seq2seq4repair_space>gene1<seq2seq4repair_space>gene2<seq2seq4repair_space>gene3<seq2seq4repair_space>gene4\n" ) ) ) , new Switch ( "duplication" , 'd' , "dup" , ( "Solves<seq2seq4repair_space>MGD<seq2seq4repair_space>problem.<seq2seq4repair_space>Minimizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>duplications<seq2seq4repair_space>required<seq2seq4repair_space>to<seq2seq4repair_space>explain<seq2seq4repair_space>" + ( "gene<seq2seq4repair_space>trees<seq2seq4repair_space>using<seq2seq4repair_space>DynaDup<seq2seq4repair_space>algorithm<seq2seq4repair_space>(Bayzid,<seq2seq4repair_space>2011).<seq2seq4repair_space>Note<seq2seq4repair_space>that<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option,<seq2seq4repair_space>" + "DynaDyp<seq2seq4repair_space>would<seq2seq4repair_space>be<seq2seq4repair_space>used<seq2seq4repair_space>*instead<seq2seq4repair_space>of*<seq2seq4repair_space>ASTRAL." ) ) ) , new FlaggedOption ( "duploss<seq2seq4repair_space>weight" , JSAP . STRING_PARSER , null , JSAP . NOT_REQUIRED , 'l' , "duploss" , ( "Solves<seq2seq4repair_space>MGDL<seq2seq4repair_space>problem.<seq2seq4repair_space>Minimizes<seq2seq4repair_space>the<seq2seq4repair_space>number<seq2seq4repair_space>duplication<seq2seq4repair_space>and<seq2seq4repair_space>losses<seq2seq4repair_space>required" + ( ( ( ( "<seq2seq4repair_space>to<seq2seq4repair_space>explain<seq2seq4repair_space>gene<seq2seq4repair_space>trees<seq2seq4repair_space>using<seq2seq4repair_space>DynaDup<seq2seq4repair_space>algorithm.<seq2seq4repair_space>Note<seq2seq4repair_space>that<seq2seq4repair_space>with<seq2seq4repair_space>this<seq2seq4repair_space>option,<seq2seq4repair_space>" + "DynaDyp<seq2seq4repair_space>would<seq2seq4repair_space>be<seq2seq4repair_space>used<seq2seq4repair_space>*instead<seq2seq4repair_space>of*<seq2seq4repair_space>ASTRAL.<seq2seq4repair_space>" ) + "Use<seq2seq4repair_space>-l<seq2seq4repair_space>0<seq2seq4repair_space>for<seq2seq4repair_space>standard<seq2seq4repair_space>(homomorphic)<seq2seq4repair_space>definition,<seq2seq4repair_space>and<seq2seq4repair_space>-l<seq2seq4repair_space>1<seq2seq4repair_space>for<seq2seq4repair_space>our<seq2seq4repair_space>new<seq2seq4repair_space>bd<seq2seq4repair_space>definition.<seq2seq4repair_space>" ) + "Any<seq2seq4repair_space>value<seq2seq4repair_space>in<seq2seq4repair_space>between<seq2seq4repair_space>weights<seq2seq4repair_space>the<seq2seq4repair_space>impact<seq2seq4repair_space>of<seq2seq4repair_space>missing<seq2seq4repair_space>taxa<seq2seq4repair_space>somewhere<seq2seq4repair_space>between<seq2seq4repair_space>these<seq2seq4repair_space>two<seq2seq4repair_space>extremes.<seq2seq4repair_space>" ) + "-l<seq2seq4repair_space>auto<seq2seq4repair_space>will<seq2seq4repair_space>automaticaly<seq2seq4repair_space>pick<seq2seq4repair_space>this<seq2seq4repair_space>weight.<seq2seq4repair_space>" ) ) ) } ) ;